scholarly journals Forest alignment with affine gaps and anchors, applied in RNA structure comparison

2013 ◽  
Vol 483 ◽  
pp. 51-67 ◽  
Author(s):  
Stefanie Schirmer ◽  
Robert Giegerich
Keyword(s):  
Rna Structure ◽  
Structure Comparison

Efficient RNA structure comparison algorithms

2017 ◽  
Vol 15 (06) ◽  
pp. 1740009 ◽  
Author(s):  
Abdullah N. Arslan ◽  
Jithendar Anandan ◽  
Eric Fry ◽  
Keith Monschke ◽  
Nitin Ganneboina ◽  
...  
Keyword(s):  
Rna Structure ◽  
Search Algorithm ◽  
Suffix Array ◽  
Rna Structures ◽  
Structure Comparison ◽  
Structure Representation ◽  
Substructure Search ◽  
Common Substructure ◽  
Search Tool ◽  
Comparison Algorithms

Recently proposed relative addressing-based ([Formula: see text]) RNA secondary structure representation has important features by which an RNA structure database can be stored into a suffix array. A fast substructure search algorithm has been proposed based on binary search on this suffix array. Using this substructure search algorithm, we present a fast algorithm that finds the largest common substructure of given multiple RNA structures in [Formula: see text] format. The multiple RNA structure comparison problem is NP-hard in its general formulation. We introduced a new problem for comparing multiple RNA structures. This problem has more strict similarity definition and objective, and we propose an algorithm that solves this problem efficiently. We also develop another comparison algorithm that iteratively calls this algorithm to locate nonoverlapping large common substructures in compared RNAs. With the new resulting tools, we improved the RNASSAC website (linked from http://faculty.tamuc.edu/aarslan ). This website now also includes two drawing tools: one specialized for preparing RNA substructures that can be used as input by the search tool, and another one for automatically drawing the entire RNA structure from a given structure sequence.

scholarly journals SETTER: web server for RNA structure comparison

2012 ◽  
Vol 40 (W1) ◽  
pp. W42-W48 ◽  
Author(s):  
Petr Čech ◽  
Daniel Svozil ◽  
David Hoksza
Keyword(s):  
Rna Structure ◽  
Web Server ◽  
Structure Comparison

scholarly journals MultiSETTER: web server for multiple RNA structure comparison

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Petr Čech ◽  
David Hoksza ◽  
Daniel Svozil
Keyword(s):  
Rna Structure ◽  
Web Server ◽  
Structure Comparison

scholarly journals RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools

2019 ◽  
Author(s):  
Marcin Magnus ◽  
Maciej Antczak ◽  
Tomasz Zok ◽  
Jakub Wiedemann ◽  
Piotr Lukasiak ◽  
...  
Keyword(s):  
Rna Structure ◽  
Structure Prediction ◽  
3D Structure ◽  
Prediction Methods ◽  
Computational Resource ◽  
Structure Comparison ◽  
Assessment Protocol ◽  
Benchmark Datasets ◽  
3D Structure Prediction ◽  
Comparison Algorithms

Abstract Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods during the succeeding challenges of RNA-Puzzles, a community-wide effort on the assessment of blind prediction of RNA tertiary structures. The RNA-Puzzles contest has shown, among others, that the development and validation of computational methods for RNA fold prediction strongly depend on the benchmark datasets and the structure comparison algorithms. Yet, there has been no systematic benchmark set or decoy structures available for the 3D structure prediction of RNA, hindering the standardization of comparative tests in the modeling of RNA structure. Furthermore, there has not been a unified set of tools that allows deep and complete RNA structure analysis, and at the same time, that is easy to use. Here, we present RNA-Puzzles toolkit, a computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods (raw, for-evaluation and standardized datasets), (ii) 3D structure normalization, analysis, manipulation, visualization tools (RNA_format, RNA_normalizer, rna-tools) and (iii) 3D structure comparison metric tools (RNAQUA, MCQ4Structures). This resource provides a full list of computational tools as well as a standard RNA 3D structure prediction assessment protocol for the community.

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